Skip to content

Commit

Permalink
Update dev docs
Browse files Browse the repository at this point in the history
  • Loading branch information
Shyue Ping Ong committed Feb 23, 2023
1 parent 83dde4e commit cfa0d96
Show file tree
Hide file tree
Showing 49 changed files with 1,378 additions and 1,208 deletions.
13 changes: 6 additions & 7 deletions docs/_modules/index.html
Original file line number Diff line number Diff line change
@@ -1,18 +1,17 @@

<!DOCTYPE html>

<html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Overview: module code &#8212; pymatgen-db 2022.5.20 documentation</title>
<title>Overview: module code &#8212; pymatgen-db 2023.2.23 documentation</title>
<link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
<link rel="stylesheet" type="text/css" href="../_static/flasky.css" />
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
<script src="../_static/doctools.js"></script>
<link rel="shortcut icon" href="../_static/favicon.ico"/>
<script src="../_static/sphinx_highlight.js"></script>
<link rel="icon" href="../_static/favicon.ico"/>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />

Expand All @@ -37,7 +36,7 @@ <h3>Navigation</h3>
<li class="right" >
<a href="../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="nav-item nav-item-0"><a href="../index.html">pymatgen-db 2022.5.20 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="../index.html">pymatgen-db 2023.2.23 documentation</a> &#187;</li>
<li class="nav-item nav-item-this"><a href="">Overview: module code</a></li>
</ul>
</div>
Expand Down Expand Up @@ -75,7 +74,7 @@ <h3 id="searchlabel">Quick search</h3>
</form>
</div>
</div>
<script>$('#searchbox').show(0);</script>
<script>document.getElementById('searchbox').style.display = "block"</script>
</div>
</div>
<div class="clearer"></div>
Expand Down
13 changes: 6 additions & 7 deletions docs/_modules/pymatgen/db/alchemy/transmuters.html
Original file line number Diff line number Diff line change
@@ -1,18 +1,17 @@

<!DOCTYPE html>

<html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pymatgen.db.alchemy.transmuters &#8212; pymatgen-db 2022.5.20 documentation</title>
<title>pymatgen.db.alchemy.transmuters &#8212; pymatgen-db 2023.2.23 documentation</title>
<link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css" />
<link rel="stylesheet" type="text/css" href="../../../../_static/flasky.css" />
<script data-url_root="../../../../" id="documentation_options" src="../../../../_static/documentation_options.js"></script>
<script src="../../../../_static/jquery.js"></script>
<script src="../../../../_static/underscore.js"></script>
<script src="../../../../_static/doctools.js"></script>
<link rel="shortcut icon" href="../../../../_static/favicon.ico"/>
<script src="../../../../_static/sphinx_highlight.js"></script>
<link rel="icon" href="../../../../_static/favicon.ico"/>
<link rel="index" title="Index" href="../../../../genindex.html" />
<link rel="search" title="Search" href="../../../../search.html" />

Expand All @@ -37,7 +36,7 @@ <h3>Navigation</h3>
<li class="right" >
<a href="../../../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="nav-item nav-item-0"><a href="../../../../index.html">pymatgen-db 2022.5.20 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="../../../../index.html">pymatgen-db 2023.2.23 documentation</a> &#187;</li>
<li class="nav-item nav-item-1"><a href="../../../index.html" accesskey="U">Module code</a> &#187;</li>
<li class="nav-item nav-item-this"><a href="">pymatgen.db.alchemy.transmuters</a></li>
</ul>
Expand Down Expand Up @@ -143,7 +142,7 @@ <h3 id="searchlabel">Quick search</h3>
</form>
</div>
</div>
<script>$('#searchbox').show(0);</script>
<script>document.getElementById('searchbox').style.display = "block"</script>
</div>
</div>
<div class="clearer"></div>
Expand Down
13 changes: 6 additions & 7 deletions docs/_modules/pymatgen/db/config.html
Original file line number Diff line number Diff line change
@@ -1,18 +1,17 @@

<!DOCTYPE html>

<html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pymatgen.db.config &#8212; pymatgen-db 2022.5.20 documentation</title>
<title>pymatgen.db.config &#8212; pymatgen-db 2023.2.23 documentation</title>
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
<link rel="stylesheet" type="text/css" href="../../../_static/flasky.css" />
<script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
<script src="../../../_static/jquery.js"></script>
<script src="../../../_static/underscore.js"></script>
<script src="../../../_static/doctools.js"></script>
<link rel="shortcut icon" href="../../../_static/favicon.ico"/>
<script src="../../../_static/sphinx_highlight.js"></script>
<link rel="icon" href="../../../_static/favicon.ico"/>
<link rel="index" title="Index" href="../../../genindex.html" />
<link rel="search" title="Search" href="../../../search.html" />

Expand All @@ -37,7 +36,7 @@ <h3>Navigation</h3>
<li class="right" >
<a href="../../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="nav-item nav-item-0"><a href="../../../index.html">pymatgen-db 2022.5.20 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="../../../index.html">pymatgen-db 2023.2.23 documentation</a> &#187;</li>
<li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li>
<li class="nav-item nav-item-this"><a href="">pymatgen.db.config</a></li>
</ul>
Expand Down Expand Up @@ -312,7 +311,7 @@ <h3 id="searchlabel">Quick search</h3>
</form>
</div>
</div>
<script>$('#searchbox').show(0);</script>
<script>document.getElementById('searchbox').style.display = "block"</script>
</div>
</div>
<div class="clearer"></div>
Expand Down
15 changes: 7 additions & 8 deletions docs/_modules/pymatgen/db/creator.html
Original file line number Diff line number Diff line change
@@ -1,18 +1,17 @@

<!DOCTYPE html>

<html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pymatgen.db.creator &#8212; pymatgen-db 2022.5.20 documentation</title>
<title>pymatgen.db.creator &#8212; pymatgen-db 2023.2.23 documentation</title>
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
<link rel="stylesheet" type="text/css" href="../../../_static/flasky.css" />
<script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
<script src="../../../_static/jquery.js"></script>
<script src="../../../_static/underscore.js"></script>
<script src="../../../_static/doctools.js"></script>
<link rel="shortcut icon" href="../../../_static/favicon.ico"/>
<script src="../../../_static/sphinx_highlight.js"></script>
<link rel="icon" href="../../../_static/favicon.ico"/>
<link rel="index" title="Index" href="../../../genindex.html" />
<link rel="search" title="Search" href="../../../search.html" />

Expand All @@ -37,7 +36,7 @@ <h3>Navigation</h3>
<li class="right" >
<a href="../../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="nav-item nav-item-0"><a href="../../../index.html">pymatgen-db 2022.5.20 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="../../../index.html">pymatgen-db 2023.2.23 documentation</a> &#187;</li>
<li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li>
<li class="nav-item nav-item-this"><a href="">pymatgen.db.creator</a></li>
</ul>
Expand Down Expand Up @@ -69,9 +68,9 @@ <h1>Source code for pymatgen.db.creator</h1><div class="highlight"><pre>

<span class="kn">import</span> <span class="nn">gridfs</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">from</span> <span class="nn">pymongo</span> <span class="kn">import</span> <span class="n">MongoClient</span>
<span class="kn">from</span> <span class="nn">monty.io</span> <span class="kn">import</span> <span class="n">zopen</span>
<span class="kn">from</span> <span class="nn">monty.json</span> <span class="kn">import</span> <span class="n">MontyEncoder</span>
<span class="kn">from</span> <span class="nn">pymongo</span> <span class="kn">import</span> <span class="n">MongoClient</span>
<span class="kn">from</span> <span class="nn">pymatgen.analysis.bond_valence</span> <span class="kn">import</span> <span class="n">BVAnalyzer</span>
<span class="kn">from</span> <span class="nn">pymatgen.analysis.local_env</span> <span class="kn">import</span> <span class="n">VoronoiNN</span>
<span class="kn">from</span> <span class="nn">pymatgen.analysis.structure_analyzer</span> <span class="kn">import</span> <span class="n">oxide_type</span>
Expand Down Expand Up @@ -848,7 +847,7 @@ <h3 id="searchlabel">Quick search</h3>
</form>
</div>
</div>
<script>$('#searchbox').show(0);</script>
<script>document.getElementById('searchbox').style.display = "block"</script>
</div>
</div>
<div class="clearer"></div>
Expand Down
19 changes: 9 additions & 10 deletions docs/_modules/pymatgen/db/matproj.html
Original file line number Diff line number Diff line change
@@ -1,18 +1,17 @@

<!DOCTYPE html>

<html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pymatgen.db.matproj &#8212; pymatgen-db 2022.5.20 documentation</title>
<title>pymatgen.db.matproj &#8212; pymatgen-db 2023.2.23 documentation</title>
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
<link rel="stylesheet" type="text/css" href="../../../_static/flasky.css" />
<script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
<script src="../../../_static/jquery.js"></script>
<script src="../../../_static/underscore.js"></script>
<script src="../../../_static/doctools.js"></script>
<link rel="shortcut icon" href="../../../_static/favicon.ico"/>
<script src="../../../_static/sphinx_highlight.js"></script>
<link rel="icon" href="../../../_static/favicon.ico"/>
<link rel="index" title="Index" href="../../../genindex.html" />
<link rel="search" title="Search" href="../../../search.html" />

Expand All @@ -37,7 +36,7 @@ <h3>Navigation</h3>
<li class="right" >
<a href="../../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="nav-item nav-item-0"><a href="../../../index.html">pymatgen-db 2022.5.20 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="../../../index.html">pymatgen-db 2023.2.23 documentation</a> &#187;</li>
<li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li>
<li class="nav-item nav-item-this"><a href="">pymatgen.db.matproj</a></li>
</ul>
Expand All @@ -54,13 +53,13 @@ <h1>Source code for pymatgen.db.matproj</h1><div class="highlight"><pre>

<span class="sd">See https://medium.com/@shyuep/a-local-materials-project-database-1ea909430c95</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">annotations</span>

<span class="kn">import</span> <span class="nn">itertools</span>

<span class="kn">import</span> <span class="nn">pymongo</span>

<span class="kn">from</span> <span class="nn">pymatgen.ext.matproj</span> <span class="kn">import</span> <span class="n">MPRester</span>
<span class="kn">from</span> <span class="nn">pymatgen.entries.computed_entries</span> <span class="kn">import</span> <span class="n">ComputedStructureEntry</span>
<span class="kn">from</span> <span class="nn">pymatgen.ext.matproj</span> <span class="kn">import</span> <span class="n">MPRester</span>


<div class="viewcode-block" id="MPDB"><a class="viewcode-back" href="../../../pymatgen.db.html#pymatgen.db.matproj.MPDB">[docs]</a><span class="k">class</span> <span class="nc">MPDB</span><span class="p">:</span>
Expand All @@ -77,7 +76,7 @@ <h1>Source code for pymatgen.db.matproj</h1><div class="highlight"><pre>
<span class="n">db</span> <span class="o">=</span> <span class="n">client</span><span class="o">.</span><span class="n">matproj</span>
<span class="bp">self</span><span class="o">.</span><span class="n">collection</span> <span class="o">=</span> <span class="n">db</span><span class="o">.</span><span class="n">entries</span>

<div class="viewcode-block" id="MPDB.create"><a class="viewcode-back" href="../../../pymatgen.db.html#pymatgen.db.matproj.MPDB.create">[docs]</a> <span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">criteria</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">property_data</span><span class="p">:</span> <span class="nb">list</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
<div class="viewcode-block" id="MPDB.create"><a class="viewcode-back" href="../../../pymatgen.db.html#pymatgen.db.matproj.MPDB.create">[docs]</a> <span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">criteria</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">property_data</span><span class="p">:</span> <span class="nb">list</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Creates the database. Typically only used once.</span>

Expand Down Expand Up @@ -170,7 +169,7 @@ <h3 id="searchlabel">Quick search</h3>
</form>
</div>
</div>
<script>$('#searchbox').show(0);</script>
<script>document.getElementById('searchbox').style.display = "block"</script>
</div>
</div>
<div class="clearer"></div>
Expand Down
13 changes: 6 additions & 7 deletions docs/_modules/pymatgen/db/query_engine.html
Original file line number Diff line number Diff line change
@@ -1,18 +1,17 @@

<!DOCTYPE html>

<html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pymatgen.db.query_engine &#8212; pymatgen-db 2022.5.20 documentation</title>
<title>pymatgen.db.query_engine &#8212; pymatgen-db 2023.2.23 documentation</title>
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
<link rel="stylesheet" type="text/css" href="../../../_static/flasky.css" />
<script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
<script src="../../../_static/jquery.js"></script>
<script src="../../../_static/underscore.js"></script>
<script src="../../../_static/doctools.js"></script>
<link rel="shortcut icon" href="../../../_static/favicon.ico"/>
<script src="../../../_static/sphinx_highlight.js"></script>
<link rel="icon" href="../../../_static/favicon.ico"/>
<link rel="index" title="Index" href="../../../genindex.html" />
<link rel="search" title="Search" href="../../../search.html" />

Expand All @@ -37,7 +36,7 @@ <h3>Navigation</h3>
<li class="right" >
<a href="../../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="nav-item nav-item-0"><a href="../../../index.html">pymatgen-db 2022.5.20 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="../../../index.html">pymatgen-db 2023.2.23 documentation</a> &#187;</li>
<li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li>
<li class="nav-item nav-item-this"><a href="">pymatgen.db.query_engine</a></li>
</ul>
Expand Down Expand Up @@ -767,7 +766,7 @@ <h3 id="searchlabel">Quick search</h3>
</form>
</div>
</div>
<script>$('#searchbox').show(0);</script>
<script>document.getElementById('searchbox').style.display = "block"</script>
</div>
</div>
<div class="clearer"></div>
Expand Down
Loading

0 comments on commit cfa0d96

Please sign in to comment.